Anders Lanzén

AZTI · Marine Research Division

Genomics is fast becoming a routine tool in medical diagnostics and cutting-edge biotechnologies. Yet, its use for environmental biomonitoring is still considered a futuristic ideal. Until now, environmental genomics was mainly used as a replacement of the burdensome morphological identification, to screen known morphologically distinguishable bioi...

A decade after environmental scientists integrated high‐throughput sequencing technologies in their toolbox, the genomics‐based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, tec...

Routine monitoring of benthic biodiversity is critical for managing and understanding the anthropogenic impacts on marine, transitional and freshwater ecosystems. However, traditional reliance on morphological identification generally makes it cost‐prohibitive to increase the ambition of monitoring programs. Metabarcoding of environmental DNA has a...

Apart from its contribution to climate change, offshore oil and gas extraction is also a potential threat to the diversity and function of marine ecosystems. Routine monitoring of the environmental status of affected areas is therefore critical for effective management. While current morphology-based monitoring is relatively time consuming, costly...

Pico‐ and nanoplankton are key players in the marine ecosystems due to their implication in the biogeochemical cycles, nutrient recycling and the pelagic food webs However, the specific dynamics and niches of most bacterial, archaeal and eukaryotic plankton remain unknown, as well as the interactions between them. Better characterisation of these i...

There is an increasing need for legislation worldwide to monitor and assess the ecological status of marine ecosystems, due to increasing pressures from human activities. The costs and time of traditional analyses are high, while methods based on molecular analysis could reduce these costs and shorten evaluation times significantly. Some biotic ind...

Multispecies and ecosystem models, which are key for the implementation of ecosystem‐based approaches to fisheries management, require extensive data on the trophic interactions between marine organisms, including changes over time. DNA metabarcoding, by allowing the simultaneous taxonomic identification of the community present in hundreds of samp...

EuropaBON EBV workflow templates The information provided here represents the EBV workflow templates collected during the EuropaBON online workshop on Essential Biodiversity Variable (EBV) workflows from 22–24 February 2023. The templates were designed to capture comprehensive descriptions about the three workflow components (data collection and s...

The information represents the EBV workflow templates collected during the EuropaBON online workshop on Essential Biodiversity Variable (EBV) workflows from 22–24 February 2023. The templates were designed to capture comprehensive descriptions about the three workflow components (data collection and sampling, data integration, and modelling) that...

Coastal environments, crucial and intricate ecosystems, face threats from human activities like pollution, eutrophication, and climate change. Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besid...

Multispecies and ecosystem models, which are key for the implementation of ecosystem-based approaches to fisheries management, require extensive data on the trophic interactions between marine organisms, including changes over time. DNA metabarcoding (the simultaneous identification of all taxa in a sample by sequencing a short DNA region) could be...

Marine harmful algal blooms (HABs), caused by various aquatic microalgae, pose significant risks to ecosystems, some socio-economic activities and human health. Traditionally managed as a public health issue through reactive control measures such as beach closures, seafood trade bans or closure of mollusc production areas, the multifaceted linkages...

Environmental DNA sequencing is the gold standard to reveal microbial community structures. In most applications, a one-fragment PCR approach is applied to amplify a taxonomic marker gene, usually a hypervariable region of the 16S rRNA gene. We used a new reverse complement (RC)-PCR-based assay that amplifies seven out of the nine hypervariable reg...

Marine sediments impacted by urban and industrial pollutants are typically exposed to reducing conditions and represent major reservoirs of toxic mercury species. Mercury methylation mediated by anaerobic microorganisms is favored under such conditions, yet little is known about potential microbial mechanisms for mercury detoxification. We used cul...

Biological invasions, resulting from human activities, exert substantial impacts on ecosystems worldwide. This review focuses on marine invasive alien species (IAS) in Europe, examining the current state, proposing strategies to address the problem, and offering recommendations for enhanced management. Effective management of biological invasions r...

Marine environments harbor a vast diversity of microorganisms, which have developed multiple strategies to adapt to stress conditions such as high salt concentrations and nutrient scarcity and, thus, are a source of natural products and high-value enzymes, as they have the ability to degrade complex polymeric substrates. These features make marine...

To avoid loss of genetic information in environmental DNA (eDNA) field samples, the preservation of nucleic acids during field sampling is a critical step. In the development of standard operating procedures (SOPs) for eDNA-based compliance monitoring, the effect of different routinely used sediment preservations on biological community structures...

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples....

Contrasting microbial composition and ecological associations in clean and polluted estuaries from the Basque Country Estuarine and coastal ecosystems are fundamentally important for global ecosystems functioning and for human activities and wellbeing. Since millions of people depend on the numerous resources they offer (i.e., fisheries, transport...

Crop harvest followed by a fallow period can act as a disturbance on soil microbial communities. Cropping systems intended to improve alpha-diversity of communities may also confer increased compositional stability during succeeding growing seasons. Over a single growing season in a long-term (18 year) agricultural field experiment incorporating co...

Microbial communities inhabiting soil-water-sediment continuum in coastal areas provide important ecosystem services. Their adaptation in response to environmental stressors, particularly mitigating the impact of pollutants discharged from human activities, has been considered for the development of microbial biomonitoring tools, but their use is s...

Environmental DNA methods such as metabarcoding have been suggested as possible alternatives or complements to the current practice of morphology-based diversity assessment for characterizing benthic communities in marine sediment. However, the source volume used in sediment eDNA studies is several magnitudes lower than that used in morphological i...

Metabarcoding of environmental DNA (eDNA) is an attractive complement to morphological methods for surveys and routine monitoring of marine sediment benthic communities. However, metabarcoding and other genetic techniques are heavily affected by choices made during sampling, processing, and analysis. Here, we investigated the effect of different eD...

Estuarine and coastal ecosystems are key in human activities, since millions of people depend on the numerous resources they offer. Therefore, these ecosystems are also exposed to a high anthropogenic pressure. Identifying and monitoring the biological indicators that allow us to evaluate the environmental impact is key for developing a sustainable...

comparsion between traditional monitoring, based on morphological taxonomy of marine macroinvertebrates, and molecular-based methods. The focus is in determining reference conditions to calculate M-AMBI based on metabarcoding, in Basque estuaries and coasts

Routine biological monitoring of the areas affected by offshore oil drilling and extraction is critical for ensuring proper environmental management. In addition to sufficient knowledge of the ecosystem affected, formalised e.g. as biotic indices of indicator species, adequate temporal and spatial resolution is also required, to provide accurate in...

Estuarine and coastal ecosystems play a fundamental role in human activities. Since millions of people depend on the numerous resources they offer (i.e., fisheries, transportation, and recreational activities), these ecosystems are also exposed to a high anthropogenic pressure. In order to better monitor and regulate such pressures, it is critical...

Monitoring and assessment of benthic communities have been routinely undertaken using morphology-based benthic indices, among which AZTI’s Marine Biotic Index (AMBI) and multivariate-AMBI (M-AMBI), are the most successful worldwide (Borja et al., 2019). They are used officially in routine monitoring in many European countries, where they have been...

Estuarine and coastal ecosystems play a fundamental role in human activities. Since millions of people depend on the resources they offer, they are also exposed to a high anthropogenic pressure. Identifying and monitoring the biological indicators that allow us to evaluate the environmental impact is key for developing a sustainable management of t...

Meromictic lakes are permanently stratified lakes that display steep gradients in salinity, oxygen and sulphur compounds tightly linked to bacterial community structure and diversity. Lake Sælenvannet is a meromictic lake located south of Bergen, Norway. The 26 m deep lake is connected to the open sea and permanently stratified into two layers sepa...

Increased exploitation of resources in sensitive marine ecosystems emphasizes the importance of knowledge regarding ecological impacts. However, current bio-monitoring practices are limited in terms of target-organisms and temporal resolution. Hence, developing new technologies is vital for enhanced ecosystem understanding. In this study, we have a...

Resistance is the capacity for a community to remain unchanged, and resilience the capacity to return to an original state, in response to disturbance. Increasing species richness may increase both dynamics. In a long-term agricultural field experiment incorporating conventional (CON), integrated (INT), conservation (CA) and organic (ORG) cropping...

Motivation: Technological advances in metatranscriptomics have enabled a deeper understanding of the structure and function of microbial communities. "Total RNA" metatranscriptomics, sequencing of total reverse transcribed RNA, provides a unique opportunity to investigate both the structure and function of active microbial communities from all thr...

Recycling of wood ash from energy production may counteract soil acidification and return essential nutrients to soils. However, wood ash amendment affects soil physicochemical parameters that control composition and functional expression of the soil microbial community. Here, we applied Total RNA-sequencing to simultaneously assess the impact of w...

A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on biodiversity and ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental DNA and RNA to cost-efficiently and accurate...

Data regarding microbial properties from long-term phytomanaged field trials are pivotal to determine long-term sustainability of phytotechnologies and to demonstrate their efficiency in ecological restoration. Here, a former part of a wood preservation site with total topsoil Cu in the 198-1169 mg Cu kg-1 range was phytomanaged with the addition o...

Despite being a promising technology for remediating metal(loid)-contaminated land, the success and effectiveness of phytotechnologies often face important challenges, e.g. selection of suited plant species, budgetary restrictions, an upcoming climate change scenario, or site-specific limitations for deploying best agronomic practices. An ultimate...

Background Metatranscriptomics has been used widely for investigation and quantification of microbial communities’ activity in response to external stimuli. By assessing the genes expressed, metatranscriptomics provides an understanding of the interactions between different major functional guilds and the environment. Here, we present a de novo ass...

Precision recall analysis of both approaches.

Background: Metatranscriptomics has been used widely for investigation and quantification of microbial communities' activity in response to external stimuli. By assessing the genes expressed, metatranscriptomics provide an understanding of the interactions between different major functional guilds and the environment. Here, we present de-novo assem...

Comparative Metatranscriptomics Workflow is a standardized and validated workflow to functionally classify quality filtered mRNA reads from metatranscriptomic or total RNA studies generated using NGS short reads. CoMW is used for classification of these reads using assembled contigs to the reference protein databases.

Recycling of wood ash from energy production may counteract soil acidification and return essential nutrients to soils. However, wood ash amendment affects soil physicochemical parameters that control composition and functional expression of the soil microbial community. Here, we applied Total RNA-sequencing to simultaneously assess the impact of w...

Technosols can be used to rehabilitate degraded land and reuse wastes. Ideally, these newly formed soils should also fulfil the main soil functions. In this study, initially, we characterized the physicochemical and microbial properties of different formulations and their ingredients (i.e., dirt from a waste recovery plant, recycled bentonite, sewa...

Livestock manure-derived amendments can be beneficial for agricultural soil quality, as they can increase the content of soil organic matter and nutrients, stimulate microbial activity and biomass, and enhance crop yield. Here, we studied the impact of six different manure-derived amendments, according to the origin (horse manure-derived vs. chicke...

The long-term recovery of soil ecological functions underlying ecosystem services should lie at the core of the assessment of any phytomanagement initiative. Soil microbial properties have demonstrated a high potential as indicators of the effectiveness of phytomanagement of metal(loid)-contaminated soils, as they are key players in many of these s...

The microbial diversity associated with diffuse venting deep-sea hydrothermal deposits is tightly coupled to the geochemistry of the hydrothermal fluids. Previous 16S rRNA gene amplicon sequencing (metabarcoding) of marine iron-hydroxide deposits along the Arctic Mid Ocean Ridge, revealed the presence of diverse bacterial communities associated wit...

In many urban catchments, the discharge of effluents from wastewater treatment plants (WWTPs), as well as untreated wastewaters (UWWs), presents a major challenge for the maintenance of river sediment and water quality. The discharge of these effluents cannot only increase the concentration of metals, nutrients and organic compounds in fluvial ecos...

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Metal resistance has been associated with antibiotic resistance due to co- or cross-resistance mechanisms. Here, metal contaminated mine soil treated with organic wastes was screened for the presence of mobile genetic elements (MGEs). The occurrence of conjugative IncP-1 and mobilizable IncQ plasmids, as well as of class 1 integrons, was confirmed...

Mountain grasslands in the Iberian Peninsula are the result of extensive grazing. However, a progressive abandonment of grazing activity is currently observed in the study region. The objective of this work was to evaluate the short-term (2 years) effects of non-grazing on the diversity and composition of plants, soil microorganisms (prokaryotes, f...

Human impact on marine benthic communities has traditionally been assessed using visible morphological traits and has focused on the macrobenthos, whereas the ecologically important organisms of the meio- and microbenthos have received less attention. DNA metabarcoding offers an alternative to this approach and enables a larger fraction of the biod...

OTU distribution table. (TSV)

Taxonomic classification and category (protists, metazoa or unknown) for representative OTU sequences. (TSV)

Rarefaction analysis of protist OTU richness for pooled samples (grey lines) and individual replicats (black lines). Mean and standard error of expected richness was calculated based on repeated random sub-samples at each read interval from replicates of the samples Fine Sand (A; n = 5), Coarse Sand (B; n = 7) and Clay (C, n = 5), after taxonomic f...

Rarefaction analysis of metazoan OTU richness for pooled samples (grey lines) and individual replicates (black lines). Mean and standard error of expected richness was calculated based on repeated random sub-samples at each read interval from replicates of the samples Fine Sand (A; n = 5), Coarse Sand (B; n = 7) and Clay (C, n = 5), after taxonomic...

Rarefaction analysis of pooled samples illustrating the effect of retaining singletons. Rarefaction curves using solid lines represent the studied dataset where singletons were retained (and correspond to Figs 1 and 2), whereas dashed lines result from rarefaction curves after removing singletons. (TIF)

Overview of sequence depth, richness and taxonomic composition (protists and metazoa) for all replicates and pooled samples. (XLSX)

Aided phytostabilization uses metal-tolerant plants, together with organic or inorganic amendments, to reduce metal bioavailability in soil while improving soil quality. The long-term effects of the following organic amendments were examined as part of an aided phytostabilization field study in an abandoned Pb/Zn mining area: cow slurry; sheep manu...

As global exploitation of available resources increases, operations extend towards sensitive and previously protected ecosystems. It is important to monitor such areas in order to detect, understand and remediate environmental responses to stressors. The natural heterogeneity and complexity of communities means that accurate monitoring requires hig...

Mountain elevation gradients are invaluable sites for understanding the effects of climate change on ecosystem function, community structure and distribution. However, relatively little is known about the impact on soil microbial communities, in spite of their importance for the functioning of the soil ecosystem. Previous studies of microbial diver...

The effect of salinity on prokaryotic community diversity in Abijata-Shalla Soda Ash Concentration Pond system was investigated by using high-throughput 16S rRNA gene 454 pyrosequencing. Surface water and brine samples from five sites spanning a salinity range of 3.4 % (Lake Abijata) to 32 % (SP230F, crystallizer pond) were analyzed. Overall, 33 pr...

Traditionally, conservation and management of mountain pastures has been managed solely on the basis of visible biota. However, microorganisms play a vital role for the functioning of the soil ecosystem and, hence, pasture sustainability. Here, we studied the links between soil microbial (belowground) community structure (using amplicon sequencing...

Parameters and taxon abundances showing significant differences with land-use (P, pastures grazed year-round; X, winter grazing only; H, non-grazed, harvested). Width of notches indicates 95% confidence intervals of the median. p-values determined by group-wise ANOVA (and verified by Tukey's range test) are given below each boxplot.